git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@116456 bc3139a8-67e5-0310-9ffc-ced21a209358
Ulrich Bodenhofer authored on 18/04/2016 15:12:00
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@@ -143,6 +143,7 @@ Institute of Bioinformatics\\ |
| 143 | 143 |
Johannes Kepler University Linz\\ |
| 144 | 144 |
A-4040 Linz, Austria |
| 145 | 145 |
\end{tabular}}}
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+\put(9.5,0.4){\makebox(0,0)[cb]{\includegraphics[height=0.8cm]{JKU_EN_noName}}}
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| 146 | 147 |
\put(19,0){\makebox(0,0)[rb]{\fontfamily{phv}\normalsize\begin{tabular}[b]{r}
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| 147 | 148 |
Tel. +43 732 2468 4520\\ |
| 148 | 149 |
Fax +43 732 2468 4539\\ |
msa
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/msa@102253 bc3139a8-67e5-0310-9ffc-ced21a209358
Sonali Arora authored on 10/04/2015 00:12:33
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new file mode 100644 |
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+% |
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+% |
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+% BIOINF document class |
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+% |
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+% last revision 2010-02-15 by Ulrich Bodenhofer |
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+% |
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+% |
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+\NeedsTeXFormat{LaTeX2e}[1995/12/01]
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+ |
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+\ProvidesClass{bioinf}[2010/02/15]
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+ |
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+\def\bioinf@basisclass{article}
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+ |
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+\newif\ifbasisclassdefined |
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+\basisclassdefinedfalse |
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+ |
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+% |
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+% declare options for three basis classes |
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+% |
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+\DeclareOption{article}{\ifbasisclassdefined
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+\ClassError{bioinf}{You may only supply one basis class.}{Remove the `article' option}
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+\fi |
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+\def\bioinf@basisclass{article}\basisclassdefinedtrue}
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+ |
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+\DeclareOption{report}{\ifbasisclassdefined
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+\ClassError{bioinf}{You may only supply one basis class.}{Remove the `report' option}
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+\fi |
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+\def\bioinf@basisclass{report}\basisclassdefinedtrue}
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+ |
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+\DeclareOption{book}{\ifbasisclassdefined
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+\ClassError{bioinf}{You may only supply one basis class.}{Remove the `book' option}
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+\fi |
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+\def\bioinf@basisclass{book}\basisclassdefinedtrue}
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+ |
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+% |
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+% forward all other options to document class article |
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+% |
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+\DeclareOption*{{\ClassError{bioinf}{Option `\CurrentOption' not supported
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+for BIOINF document class.}{Remove the `\CurrentOption' option}}}
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+ |
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+% |
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+% process options |
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+% |
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+\ProcessOptions\relax |
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+ |
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+% |
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+% load document class article (always with options a4paper and titlepage) |
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+% |
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+\LoadClass[a4paper,11pt,twoside]{\bioinf@basisclass}
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+ |
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+\typeout{=============================================================}%
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+\typeout{BIOINF document class loaded with basis class '\bioinf@basisclass'}%
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+\typeout{=============================================================}%
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+ |
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+% |
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+% font customizations |
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+% |
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+\renewcommand{\encodingdefault}{T1}
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+\renewcommand{\rmdefault}{ptm}
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+\renewcommand{\sfdefault}{phv}
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+\renewcommand{\ttdefault}{cmtt}
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+\fontencoding{T1}\selectfont
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+ |
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+% |
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+% customization of item marks |
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+% |
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+\renewcommand{\labelitemi}{\rule[0.2ex]{0.8ex}{0.8ex}}
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+\renewcommand{\labelitemii}{$\m@th\bullet$}
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+ |
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+% |
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+% include of additional packages |
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+% |
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+\RequirePackage{color}
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+\RequirePackage{graphicx}
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+\RequirePackage{ifthen}
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+ |
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+% |
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+% setup of page format |
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+% |
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+\setlength{\evensidemargin}{-1in}
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+\setlength{\oddsidemargin}{-1in}
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+\setlength{\topmargin}{-1in}
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+\addtolength\evensidemargin{30mm}
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+\addtolength\oddsidemargin{30mm}
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+\addtolength\topmargin{28mm}
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+\setlength{\textwidth}{150mm}
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+\setlength{\headheight}{12pt}
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+\setlength{\headsep}{8mm}
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+\setlength{\textheight}{222mm}
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+ |
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+\ifx\pdfoutput\undefined |
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+\relax |
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+\else |
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+\setlength{\pdfpagewidth}{21cm}
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+\setlength{\pdfpageheight}{29.7cm}
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+\fi |
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+ |
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+% |
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+% setup of customized headings style and listings |
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+% |
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+\input{bioinf-\bioinf@basisclass.txi}
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+ |
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+% |
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+% set page style |
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+% |
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+\pagestyle{headings}
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+ |
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+% |
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+% adjust parskip |
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+% |
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+\setlength{\parskip}{5pt plus 2pt minus 1pt}
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+ |
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+% |
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+% define colors and color commands |
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+% |
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+\definecolor{biowh}{rgb}{1.00,1.00,1.00}
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+\definecolor{biobl}{rgb}{0.00,0.00,0.00}
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+\definecolor{bioaz}{rgb}{0.204,0.325,0.631}
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+\definecolor{biove}{rgb}{0.24,0.63,0.37}
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+\definecolor{bioli}{rgb}{0.667,0.9333,0.667}
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+ |
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+\newcommand{\blue}{\color{bioaz}}
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+\newcommand{\green}{\color{biove}}
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+ |
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+% |
|
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+% define BIOINF title page commands |
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+% |
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+\newcommand{\customtitlepage}[2]{%
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+\thispagestyle{empty}
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+#2 |
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+\vfill |
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+\noindent\makebox[0pt][l]{%
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+\setlength{\unitlength}{1cm}
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+\begin{picture}(0,0)(2,2.4)
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+%\put(0,25.5){\makebox(0,0)[lb]{\color{bioli}\rule{19cm}{2.2cm}}}
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+\put(19,25.5){\makebox(0,0)[rb]{\includegraphics[width=19cm]{bioinf-bar}}}
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+\put(0.3,26.0){\makebox(0,0)[l]{\color{bioaz}\fontfamily{phv}\bfseries\large%
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+Institute of Bioinformatics, Johannes Kepler University Linz}} |
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+\put(0.3,26.9){\makebox(0,0)[l]{\color{bioaz}\fontfamily{phv}\bfseries\Huge #1}}
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+\put(0,1.6){\makebox(0,0)[lb]{\color{bioli}\rule{19cm}{1mm}}}
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+\put(0,0){\makebox(0,0)[lb]{\fontfamily{phv}\normalsize\begin{tabular}[b]{l}
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+Institute of Bioinformatics\\ |
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+Johannes Kepler University Linz\\ |
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+A-4040 Linz, Austria |
|
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+\end{tabular}}}
|
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+\put(19,0){\makebox(0,0)[rb]{\fontfamily{phv}\normalsize\begin{tabular}[b]{r}
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+Tel. +43 732 2468 4520\\ |
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+Fax +43 732 2468 4539\\ |
|
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+http://www.bioinf.jku.at |
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+\end{tabular}}}
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+%\put(0,24.5){\makebox(0,0)[lt]{\noindent\begin{minipage}{19cm}
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+%#2 |
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+%\end{minipage}}}
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+\end{picture}}\newpage}
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+ |
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+\def\bioinf@number{}
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+\def\bioinf@keywords{}
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+\def\bioinf@abstract{}
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+\def\bioinf@citation{}
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+\def\bioinf@affiliation{}
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+ |
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+\newcommand{\affiliation}[1]{\def\bioinf@affiliation{#1}}
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+\newcommand{\pubnumber}[1]{\def\bioinf@number{#1}}
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+\newcommand{\setkeywords}[1]{\def\bioinf@keywords{#1}}
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+\newcommand{\setabstract}[1]{\def\bioinf@abstract{#1}}
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+\newcommand{\setcitation}[1]{\def\bioinf@citation{#1}}
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+\newcommand{\affilmark}[1]{\textsuperscript{\scriptsize #1}}
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+ |
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+\newcommand{\doi}[1]{%
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+\ifx\href\undefined |
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+doi:#1 |
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+\else |
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+\href{http://dx.doi.org/#1}{doi:#1}
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+\fi} |
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+ |
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+\newcommand{\email}[1]{\ifx\href\undefined
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+{\em #1}
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+\else |
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+\href{mailto:#1}{{\em #1}}
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+\fi} |
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+ |
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+\newcommand{\reporttitlepage}[1]{\customtitlepage{#1}{%
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+\mbox{ }
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+\vfill |
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+\begin{center}
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+\sffamily\bfseries\LARGE\@title |
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+\end{center}
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+ |
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+\begin{center}
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+{\sffamily\bfseries\large\@author}\\[2mm]
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+\ifx\@empty\bioinf@affiliation |
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+ \relax |
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+\else |
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+{\sffamily\normalsize\bioinf@affiliation}
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+\end{center}
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+\fi |
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+ |
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+\vspace{1.5cm}
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+ |
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+\ifthenelse{\equal{}{\bioinf@abstract}}{%
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+ \relax |
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+}{%
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+ \centerline{\rule{15cm}{1pt}}\vspace{2mm}
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+ \centerline{\begin{minipage}[b]{15cm}
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+ \noindent{\bf Abstract --- } \bioinf@abstract
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+ \end{minipage}}
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+ \ifx\@empty\bioinf@keywords |
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+ \vspace{-1.5mm}\centerline{\rule{15cm}{1pt}}
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+ \fi |
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+} |
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+ |
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+\ifthenelse{\equal{}{\bioinf@keywords}}{%
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+ \relax |
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+}{%
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+ \ifx\@empty\bioinf@abstract |
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+ \centerline{\rule{15cm}{1pt}}\vspace{2mm}
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+ \else |
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+ \vspace{5mm}
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+ \fi |
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+ \centerline{\begin{minipage}[b]{15cm}
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+ \noindent{\bf Key words --- } \bioinf@keywords
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+ \end{minipage}}
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+ \vspace{-1.5mm}\centerline{\rule{15cm}{1pt}}
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+} |
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+ |
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+\ifthenelse{\equal{}{\bioinf@citation}}{%
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+ \relax |
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+}{%
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+ \vspace{2cm}
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+ \centerline{\begin{minipage}[b]{15cm}
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+ \noindent{\bf Citation: } \bioinf@citation
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+ \end{minipage}}
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+} |
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+ |
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+\vfill}} |
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+ |
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+\newcommand{\researchreporttitlepage}{\reporttitlepage{Research Report \bioinf@number}}
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+ |
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+\newcommand{\techreporttitlepage}{\reporttitlepage{Technical Report \bioinf@number}}
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+ |
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+\newcommand{\preprinttitlepage}{\reporttitlepage{Publication Preprint}{}}
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+ |
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+\newcommand{\reprinttitlepage}{\reporttitlepage{Publication Reprint}{}}
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+ |
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+\newcommand{\manualtitlepage}[1][]{\customtitlepage{Software Manual}{%
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+\mbox{ }
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+\vfill |
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+\begin{center}
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+\sffamily\bfseries\LARGE\@title |
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+\end{center}
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+ |
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+\ifthenelse{\equal{\@author}{}}{}{\begin{center}
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+{\sffamily\bfseries\large\@author}\\[2mm]
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+\ifx\@empty\bioinf@affiliation |
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+ \relax |
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+\else |
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+{\sffamily\normalsize\bioinf@affiliation}
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+\end{center}
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+\fi} |
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+ |
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+\vspace{1cm}
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+ |
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+\begin{center}
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+{\Large\sffamily\bfseries #1}
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+\end{center}
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+ |
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+\vfill |
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+ |
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+\mbox{ }}}
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+ |
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+\newcommand{\lecturenotestitlepage}[1][]{\customtitlepage{Lecture Notes}{%
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+\ifthenelse{\equal{#1}{}}{%
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+\vspace*{2cm}
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+\begin{center}
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+\sffamily\bfseries\huge \@title |
|
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+\end{center}
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+ |
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+\vspace{2cm}
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+ |
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+\begin{center}
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+\sffamily\bfseries\Large \@author |
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+\end{center}
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+ |
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+\vfill |
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+ |
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+\mbox{ }}{%
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+{\LARGE\sffamily\bfseries\mbox{ }
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+ |
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+\vfill |
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+ |
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+\begin{center}
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+#1 |
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+\end{center}
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+\vfill |
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+ |
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+\vfill |
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+ |
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+\mbox{ }}}}}
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+ |
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+\newcommand{\copyrightpage}[1][]{%
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+\clearpage |
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+\mbox{ }
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+ |
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+\vfill |
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+ |
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+\vfill |
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+ |
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+\noindent{\large \textcircled{c}
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+\ifthenelse{\equal{#1}{}}{%
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+\@author}{%
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+#1}}\\[7mm] |
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+\noindent \BIOINFCopyrightNotice\thispagestyle{empty}
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+ |
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+\vfill |
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+ |
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+\mbox{ }
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+\clearpage} |
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+ |
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+\newcommand{\BIOINFCopyrightNotice}{This material, no matter whether in printed or electronic
|
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+form, may be used for personal and educational use only. Any |
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+reproduction of this manuscript, no matter whether as a whole or in |
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| 322 |
+parts, no matter whether in printed or in electronic form, requires |
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+explicit prior acceptance of the author.} |
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+ |
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+\endinput |
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| 326 |
+% |
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| 327 |
+% end of scch-tr.cls |
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+% |